Re: [AMBER] sander job crashed

From: Ben Roberts <>
Date: Fri, 8 Jul 2011 07:59:23 -0400

Hi Mustafa,

On 8/07/2011, at 4:02 AM, MUSTAFA BUGHIO wrote:

> Thanks beb
> I am new user of AMBER, i have given input file named for
> minimization of my protein. Its pentamer homology model which i have
> neutralised by adding charges and solvated in TIP3PBOX 10A. Yes you are
> right that it should be minimized before MD run that's what i am trying to
> do but following error is reported.
> Other than AMBER minimization i tried to minimize via Sybyl and Modeller
> optimization program. I found that after minimization my proteins Beta
> sheets were completely disappeared and formed all loops. But when i
> minimized only Monomer by same input file it had removed bad clashes and my
> PDB was better refined therefore i am trying to repeat same procedure with
> pentamer which gives VDWAALS error.

I trust that you've ensured your monomers (in the pentamer) aren't superimposed.

> Is there any process to minimize VDW forces other than AMBER. If giving
> cutoff value can help me. as i have not given any cutoff in my input file.

Please provide your input file. The cutoff is probably not an issue in this case.
A default value for the cutoff will be used if it's not explicitly set.


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Received on Fri Jul 08 2011 - 05:00:03 PDT
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